GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21725 in Rhodobacter viridis JA737

Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate WP_110806871.1 C8J30_RS16150 ATP-binding cassette domain-containing protein

Query= reanno::pseudo3_N2E3:AO353_21725
         (265 letters)



>NCBI__GCF_003217355.1:WP_110806871.1
          Length = 259

 Score =  253 bits (645), Expect = 4e-72
 Identities = 132/254 (51%), Positives = 180/254 (70%), Gaps = 4/254 (1%)

Query: 11  ASQALLEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGG 70
           A+  +L  +D+HK +G  EVLKG+ L  +  +V++++G+SGSGK+T LRC+N LE    G
Sbjct: 6   ATDLVLSAQDIHKSFGAQEVLKGITLGARNHDVISILGTSGSGKSTFLRCLNCLEVPNSG 65

Query: 71  QILLDGESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVK 130
            + + GE I +   NG+     ++ I + R   GM FQQFNL+ H T L+NV  G ++VK
Sbjct: 66  SVAVHGEEIVFR--NGRI--GDQRQIERLRRHLGMVFQQFNLWTHRTVLENVMEGPVQVK 121

Query: 131 KLHKDEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSA 190
           ++ K EA  LAE  L RVGL +R  HYP  LSGGQQQRVAIARA+AM P ++LFDE TSA
Sbjct: 122 RMPKAEARDLAEGLLARVGLADRMGHYPAMLSGGQQQRVAIARALAMEPDVILFDEPTSA 181

Query: 191 LDPELVGEVLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFER 250
           LDPELVGEVL V++ LA +G TM++VTHEM FA +VS ++VF+N+GRI EQGPP++LF+ 
Sbjct: 182 LDPELVGEVLKVMQDLAAEGRTMIVVTHEMAFARDVSTEVVFLNEGRIAEQGPPEKLFDH 241

Query: 251 PQSPRLAEFLKNTR 264
           P++   A F+  TR
Sbjct: 242 PETEVFARFISKTR 255


Lambda     K      H
   0.319    0.135    0.379 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 198
Number of extensions: 6
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 265
Length of database: 259
Length adjustment: 25
Effective length of query: 240
Effective length of database: 234
Effective search space:    56160
Effective search space used:    56160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory